Craven SJ, Condon SGF, Senes A
“A model of the interactions between the FtsQLB and the FtsWI peptidoglycan synthase complex in bacterial cell division”
2022, under review
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Díaz Vázquez G, Cui Q, Senes A
“Thermodynamic analysis of the GASright transmembrane motif supports energetic model of dimerization”
Biophysical J. 2022 in press, doi:10.1016/j.bpj.2022.11.018
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Craven SJ, Condon SGF, Díaz Vázquez G, Cui Q, Senes A
“The coiled-coil domain of Escherichia coli FtsLB is a structurally detuned element critical for modulating its activation in bacterial cell division ”
J. Biol. Chem.2022 298 101460
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Kaur H, Jamalidinan F, Condon SGF, Senes A, Hoskins AA
“Analysis of spliceosome dynamics by maximum likelihood fitting of dwell time distributions”
Methods 2019 153, 13-21
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Niemann MCE, Weber H, Hluska T, Leonte G, Anderson SM, Novak O, Senes A, Werner T
“The cytokinin oxidase/dehydrogenase CKX1 is a membrane-bound protein requiring homooligomerization in the endoplasmic reticulum for its cellular activity”
Plant Physiology 2018 176, 2024-39
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Condon SGF*, Mahbuba DA*, Armstrong CR, Diaz-Vazquez G, Craven SJ, LaPointe LM, Khadria AS, Chadda R, Crooks JA, Rangarajan N, Weibel DB, Hoskins AA, Robertson JL, Cui Q, Senes A
“The FtsLB sub-complex of the bacterial divisome is a tetramer with an uninterrupted FtsL helix linking the transmembrane and periplasmic regions”
J. Biol. Chem. 2018 293, 1623-41 (*authors contributed equally)
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Anderson SM*, Mueller BK*, Lange EJ and Senes A

“Combination of Cα-H hydrogen bonds and van der Waals packing modulates the stability of GxxxG-mediated dimers in membranes”

J Am Chem Soc. (2017) 139, 15774-83 (*authors contributed equally)
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Guo X, Niemi NM, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, Higbee AJ, Russell JD, Senes A, Coon JJ, and Pagliarini DJ
“Ptc7p dephosphorylates select mitochondrial proteins to enhance metabolic function”
Cell Reports (2017) 18, 307-13
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Armstrong CR, Senes A
“Screening for transmembrane association in divisome proteins using TOXGREEN, a high-throughput variant of the TOXCAT assay”
Biochim. Biophys. Acta (2016) 1858, 2573-83
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Barth P, Senes A
“Toward high-resolution computational design of the structure and function of helical membrane proteins”
Nat Struct Mol Biol (2016) 23, 475-80
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Zhang Z, Subramaniam S, Kale J, Liao C, Huang B, Brahmbhatt H, Condon SGF, Lapolla SM, Hays, FA, Ding J, He F, Zhang XC, Li J, Senes A, Andrews DW, Lin J
“BH3-in-groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes”
EMBO J (2016) 35, 208-36
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Khadria AS, Senes A
“Fluorophores, environments and quantification techniques in the analysis of transmembrane helix interaction using FRET”
Biopolymers (2015) 104, 247-264
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Ma G, Wei M, He L, Liu C, B Wu , Zhang S, Jing J, Liang X, Senes A, Tan P, Li S, Sun A, Bi Y, Zhong L, Si H, Shen Y, Li M, Lee MS, Zhou W, Wang J, Wang Y and Zhou Y
“Inside-out Ca2+ signaling prompted by STIM1 conformational switch”
Nat. Commun. (2015) 6, 7826

Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ and Senes A
“A Gly-zipper motif mediates homo-dimerization of the transmembrane domain of the mitochondrial kinase ADCK3”
J Am Chem Soc (2014) 136, 14068-77

Subramaniam S, Senes A
“Backbone dependency further improves side chain prediction efficiency in the Energy-Based Conformer Library (bEBL)”
Proteins (2014) 81, 3177-3187

Mueller BK*, Subramaniam S*, Senes A
“A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα-H hydrogen bonds”
Proc Natl Acad Sci USA (2014) 111, E888-95 (*authors contributed equally)

Khadria AS, Senes A
“The transmembrane domains of the bacterial cell division proteins FtsB and FtsL form a stable high-order oligomer”
Biochemistry 2013 52, 7532-41

Khadria A and Senes A
“Measurement of transmembrane peptide interaction in liposomes using Forster Resonance Energy Transfer (FRET)”
Methods Mol. Biol. 2013 1063, 19-36

LaPointe LM, Taylor KC, Subramaniam S, Khadria A, Rayment I and Senes A
“Structural organization of FtsB, a transmembrane protein of the bacterial divisome”
Biochemistry 2013 52, 2574-85

Subramaniam S and Senes A
“An Energy-Based conformer library for side chain optimization: improved prediction and adjustable sampling”
Proteins 2012 80, 2218-34

Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A
“Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)”
J Comput. Chem. 2012 33(20), 1645-61

Hsin J, LaPointe LM, Kazy A, Chipot CJ, Senes A, Schulten K
“Oligomerization State of Photosynthetic Core Complexes is Correlated with the Dimerization Affinity of a Transmembrane Helix”
J Am Chem Soc. 2011 133(35), 14071-81

Senes A
“Computational Design of Membrane Proteins”
Curr Opin Struct Biol. 2011 21(4), 460-6

Subramaniam S, Natarajan S, and Senes A
“A Machine Learning based Approach to Improve Protein Sidechain Optimization”
ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB) 2011, 478-480


Korendovych IV, Senes A, Kim YH, Lear JD, Fry HC, Therien MJ, Blasie JK, Walker FA, DeGrado, WF “De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex” J Am Chem Soc. 2010 132(44), 15516-8

Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF. “Consensus motif for integrin transmembrane helix association.” Proc Natl Acad Sci USA/i> 2010 107(2), 703-8

McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. “Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays.” J Am Chem Soc. 2008 130(36), 11921-7

Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA. “Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores.” J Phys Chem A. 2007 111(30), 6977-90

Senes A, Chadi DC, Law PB, Walters RF, Nanda V, DeGrado WF. “E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes, derivation and applications to determining the orientation of transmembrane and interfacial helices.” J Mol Biol. 2007 366(2), 436-48

Fang C, Senes A, Cristian L, DeGrado WF, Hochstrasser RM. “Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer.” Proc Natl Acad Sci USA 2006 103(45), 16740-5

Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. “Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.” Q Rev Biophys. 2004 37(2), 121-46

Senes A, Engel DE, DeGrado WF. “Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs.” Curr Opin Struct Biol. 2004 14(4), 465-79

Engelman DM, Chen Y, Chin CN, Curran AR, Dixon AM, Dupuy AD, Lee AS, Lehnert U, Matthews EE, Reshetnyak YK, Senes A, Popot JL. “Membrane protein folding: beyond the two stage model.” FEBS Lett. 2003 555(1), 122-5

Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. “GeneCensus, genome comparisons in terms of metabolic pathway activity and protein family sharing.” Nucleic Acids Res. 2002 30(20), 4574-82

Senes A, Ubarretxena-Belandia I, Engelman DM. “The Calpha —H…O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions.” Proc Natl Acad Sci USA 2001 98(16), 9056-61

Senes A, Gerstein M, Engelman DM. “Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.” J Mol Biol. 2000 296(3), 921-36

Formato M, Senes A, Soccolini F, Coinu R, Cherchi GM. “A reversed phase HPLC method for the simultaneous determination of all monosaccharides contained in galactosaminoglycan isomers from human aorta proteoglycans.” Carbohydr Res. 1994 255, 27-39